In an extraordinary letter, Francis also summoned Chile's bishops to the Vatican for an emergency meeting in the coming weeks to discuss the scandal, which has badly tarnished his reputation and that of the Chilean church.
Monsignor Scicluna visited Chile as prosecutor of the Vatican to investigate into bishop of Osorno Juan Barros, accused of complicity with ousted priest Fernando Karadima for pedophilia and sexual abuse.
Francis strongly defended the bishop during his January visit to Chile despite accusations by victims that Barros had witnessed and ignored their abuse.
Protesters and victims said Bishop Barros is guilty of protecting Father Karadima and was physically present while some of the abuse was going on.
The Vatican orders up such emergency visits only on rare occasions, such as when American bishops were summoned in 2002 after the clerical sex abuse scandal exploded in the US and in 2010 when Irish bishops received a comprehensive Vatican dressing down for their botched handling of abuse cases.
The Vatican stripped Karadima of serving in the ministry because he allegedly abused minors.
While in Chile, Archbishop Scicluna interviewed some 64 people related to the accusations and compiled an report that is some 2,300 pages long, which he delivered to Pope Francis March 20.
Francis sent the Vatican's most respected sex abuse investigator, Archbishop Charles Scicluna, to investigate allegations of a sex abuse cover-up by Barros, a protege of Karadima.
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Francis overrode their concerns and appointed Barros bishop of the southern Chilean diocese of Osorno in 2015, saying the church had investigated the claims against him and found them to be baseless.
The Argentine pontiff said that he was convinced of Barros' innocence and demanded "proof" of abuse before he would speak out against him.
Pope Francis has recently written a letter to Chile's bishops following a scandal over his robust defense against the bishop accused of watching and ignoring sex abuse by Chile's most notorious predator man.
The president of the Episcopal Conference of Chile, Bishop Santiago Silva, said that the church "had not done enough" in the case. Pope Francis has backed him, and has refused to allow him to step down from his post, though the bishop has submitted a letter of resignation multiple times. Boston's Cardinal Sean O'Malley, head of the pope's sex abuse commission, said in a statement that the words were a "source of great pain" for survivors. It is unclear whether the pope actually read that letter.
Before going to Santiago Feb. 19 to interview witnesses related to the Bishop Barros accusations, Archbishop Scicluna stopped in NY to interview Cruz.
Archbishop Scicluna is a well-regarded Vatican expert on sex abuse appeals cases. The letter also said that Barros witnessed the abuses and played a major role in their cover-up. Earlier this year, the Marist Brothers began a canonical investigation of allegations of sexual abuse in Chile by some of its members.
Jaime Coiro, spokesman for the Chilean bishops' conference, said the pope wrote the letter after receiving Scicluna's report.
"Now more than ever we can not fall back into the temptation of verbiage or stain in 'universals, ' he said, and told the bishops to look to Christ in the coming days and weeks".